Overview

The biology/biotechnology in agriculture, medicine, industry and environment have been contributing to breakthroughs in science and technology and the development of the Vietnamese economy at the moment and in the future. Vietnam School of Biology (VSOB) was established in the series of schools in ICISE, Quy Nhon, Binh Dinh and sponsored by Rencontres du Vietnam. The main role of VSOB is to provide new and modern knowledge, techniques and approaches in the field of biology/biotechnology to undergraduates, postgraduates and young scientists in Vietnam and abroad for enhancing scientific research capacity. Additionally, VSOB is also the venue for meetings/workshops/conferences between Vietnamese and worldwide scientists in the field of biology/biotechnology.

---

The VSOB-2 will be devoted to a training course at theoretical and practical levels with the topic: "Genomic analysis of microbial pathogens using illumina and Nanopore technologies".

1.Course description

Short-read sequencing using Illumina technology has been widely used for whole genome sequencing of microbial pathogens because of the low cost and high accuracy. However, Illumina sequencing-only draft genomes may fail to identify long repeat regions and miss information on certain genomic regions. Long-read sequencing technologies provide greater overlap between reads that enable complete assemblies of microbial genomes. Nanopore sequencing technology can produce reads with an average length greater than 16 Kb which are able to capture long repeat regions. Compared to short-read sequencing, Nanopore sequencing is currently limited by the high error rates. Combination of long-read and short-read sequencing offer a further advantage in generate high-quality whole genome assemblies and will be routinely offered for genome analysis.

The purpose of the workshop is to enhance the knowledge, appreciation, and application of Illumina and Nanopore sequencing related to microbial pathogens. Participants will be able to process raw data from Illumina and Oxford Nanopore sequence data using different bioinformatics tools to produce a high-quality microbial genome sequence.

2. Brief background

Microorganisms can be found in diverse environments including in clinical, environmental or food samples and have the potential to cause disease in plants, animals and humans. Traditionally, microbial pathogens have been detected using culture-based methods or immunological assays. Next-generation sequencing technologies have provided new insights into microbial genome characteristics, molecular mechanisms underlying pathogenicity, as well as the relationship between genotype and phenotype.

3. Course objectives

• For wet-lab, students will be able to explore sequencing protocols and laboratory procedures such as DNA extraction, library preparation, Nanopore sequencing in clinical or food samples; including the need for appropriate and stringent quality control.
• For dry-lab, students are familiar with and can use and apply modern bioinformatics technologies used in genomic research. Processing of raw sequencing data from both short-read and long-read sequencing, including quality control, de novo assembly from raw reads to contigs, genome annotation.

4. Location

ICISE center, located by the sea and surrounded by mountains, about 6km from the city of Quy Nhon. The lecture hall is equipped with a video projector, a blackboard, audio system, wireless connection. ICISE has a nice, quiet campus with coconut trees and a beautiful beach.

5. Schedule

Time: 9-11/12/2023

Key dates:

• 30/4/2023: VSOB-2 registration open
• 20/10/2023: VSOB-2 registration deadline
• 24/10/2023: Announcement of selected VSOB-2 participants
• 08/12/2023: Welcome all participants to Quy Nhon, Binh Dinh, Vietnam
• 09/12/2023: Opening ceremony of VSOB-2
• 11/12/2023: Closing ceremony of VSOB-2

6. Criteria selection

Target audience: The workshop is targeting strongly interested graduates, postgraduates, staff bioinformaticians and PIs who are currently executing or planning to conduct genomic studies in the near future, especially in microbial pathogens.

Prerequisites:

You will also require your own laptop computer. Minimum requirements: 1024x768 screen resolution, 1.5GHz CPU, 2GB RAM, 10GB free disk space, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements).

---

Official Languages

Vietnamese

Registration fee: 3.000.000 VND

The registration fee must be paid at:
Bank account: Rencontres du Vietnam
Account number: 0051000521912
Bank: Vietcombank
Branch: Quy Nhon City, Binh Dinh province, chi nhánh TP Quy Nhơn
Transfer content: Name_VSOB2023

---

Financial Support:

Participants are expected to cover their own travel. The VSOB-2 will cover accommodation, foods and local hospitality for all selected participants during the event in ICISE.

Inquiry or cancellation should be sent to vsob.icise@gmail.com

Organizer